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- PDB-4b85: Mus musculus Acetylcholinesterase in complex with 4-Chloranyl-N-(... -

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Basic information

Entry
Database: PDB / ID: 4b85
TitleMus musculus Acetylcholinesterase in complex with 4-Chloranyl-N-(2- diethylamino-ethyl)-benzenesulfonamide
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / INHIBITOR
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / choline metabolic process / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / laminin binding / side of membrane / synaptic cleft / synapse assembly / collagen binding / response to insulin / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nuclear envelope / presynaptic membrane / positive regulation of cold-induced thermogenesis / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / synapse / dendrite / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-B3W / DI(HYDROXYETHYL)ETHER / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsAndersson, C.D. / Forsgren, N. / Akfur, C. / Allgardsson, A. / Berg, L. / Qian, W. / Ekstrom, F. / Linusson, A.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Divergent Structure-Activity Relationships of Structurally Similar Acetylcholinesterase Inhibitors.
Authors: Andersson, C.D. / Forsgren, N. / Akfur, C. / Allgardsson, A. / Berg, L. / Engdahl, C. / Qian, W. / Ekstrom, F.J. / Linusson, A.
History
DepositionAug 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
B: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,81517
Polymers120,4682
Non-polymers2,34715
Water11,944663
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-35.5 kcal/mol
Surface area37970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.527, 112.892, 226.496
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein ACETYLCHOLINESTERASE / / ACHE


Mass: 60233.984 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PCDNA3.1 / Cell line (production host): HEK 293F / Production host: HOMO SAPIENS (human) / References: UniProt: P21836, acetylcholinesterase
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 676 molecules

#2: Chemical ChemComp-B3W / 4-chloranyl-N-[2-(diethylamino)ethyl]benzenesulfonamide


Mass: 290.809 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19ClN2O2S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 663 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 7 / Details: 27-31 % (W/V) PEG750MME, 0.1 M HEPES PH 7.0-7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→29.2 Å / Num. obs: 119406 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 5.8 % / Biso Wilson estimate: 37.26 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1J06

1j06


Resolution: 2.1→29.189 Å / SU ML: 0.29 / σ(F): 1.36 / Phase error: 19.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2059 2414 2 %
Rwork0.1767 --
obs0.1773 119303 99.82 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.925 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 43 Å2
Baniso -1Baniso -2Baniso -3
1-0.312 Å20 Å20 Å2
2--1.8853 Å20 Å2
3----2.1973 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8326 0 137 663 9126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088850
X-RAY DIFFRACTIONf_angle_d1.11912081
X-RAY DIFFRACTIONf_dihedral_angle_d15.8653266
X-RAY DIFFRACTIONf_chiral_restr0.0821293
X-RAY DIFFRACTIONf_plane_restr0.0051577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14290.27531510.25816767X-RAY DIFFRACTION100
2.1429-2.18940.28381490.24216800X-RAY DIFFRACTION100
2.1894-2.24030.28471570.22726771X-RAY DIFFRACTION100
2.2403-2.29640.25331470.21066832X-RAY DIFFRACTION100
2.2964-2.35840.2411480.21186817X-RAY DIFFRACTION100
2.3584-2.42780.24831370.20396832X-RAY DIFFRACTION100
2.4278-2.50610.25471070.19516869X-RAY DIFFRACTION100
2.5061-2.59560.24681560.18966819X-RAY DIFFRACTION100
2.5956-2.69950.21791460.18516851X-RAY DIFFRACTION100
2.6995-2.82220.23351410.17876874X-RAY DIFFRACTION100
2.8222-2.97090.24211350.18396857X-RAY DIFFRACTION100
2.9709-3.15680.22011500.18466881X-RAY DIFFRACTION100
3.1568-3.40020.20391310.18676894X-RAY DIFFRACTION100
3.4002-3.74180.20781410.17486954X-RAY DIFFRACTION100
3.7418-4.28180.14981400.1446945X-RAY DIFFRACTION100
4.2818-5.3890.15231370.13247041X-RAY DIFFRACTION100
5.389-29.19170.19091410.18327085X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6366-0.0602-0.19650.3873-0.2451.5299-0.0564-0.0543-0.04180.0322-0.0032-0.04150.11190.0823-0.00040.14260.02090.00150.10240.03160.166734.379611.247423.6276
20.3751-0.13680.5603-0.1741-0.36821.2898-0.0880.0558-0.0324-0.0709-0.01960.071-0.0867-0.2515-0.00080.25420.0088-0.01420.2418-0.01390.262118.838517.64516.7079
30.1723-0.2545-0.04110.575-0.0720.14830.04540.0205-0.3059-0.1614-0.00760.6150.3885-1.02970.02660.3256-0.20360.00660.5579-0.02180.43127.37431.202714.1137
40.1085-0.21380.2150.4726-0.28760.27020.0919-0.1045-0.0118-0.282-0.13160.17410.0873-0.144-0.01170.2755-0.0302-0.06760.4088-0.04590.289417.33816.3857-0.5931
50.1036-0.06640.08850.48840.06450.23570.08050.4036-0.1227-0.3939-0.16880.15840.003-0.178-0.0460.28610.0783-0.09190.4707-0.14650.3184-4.08685.7336-61.1897
60.20210.12820.05350.36770.52841.11180.0990.258-0.1423-0.0507-0.19180.12110.2513-0.2028-0.01610.27980.0033-0.06250.3217-0.11340.2862.43220.1139-52.7859
70.4581-0.48430.30210.55970.71531.52360.10240.1021-0.0053-0.0247-0.00980.05390.030.14710.05620.2180.0081-0.02880.2793-0.05230.247212.52995.4773-48.3994
80.9223-0.09450.40490.35910.30691.0010.22390.3140.16840.11950.0240.13440.34570.33170.16660.31090.0187-0.09040.1577-0.10020.213916.70492.699-38.5321
90.32970.16930.03660.1204-0.03570.11620.2003-0.1294-0.04850.1015-0.09520.00670.57560.0384-0.00070.5368-0.0351-0.0970.2589-0.03370.27514.1684-4.9116-17.7905
100.2156-0.3011-0.07250.42020.39340.89290.1259-0.04950.03130.169-0.17070.0955-0.0273-0.2341-00.2206-0.05280.00190.2881-0.05490.2955-2.59448.5664-32.8495
110.0552-0.053-0.11730.1940.08640.23230.0533-0.15490.1490.0878-0.01770.1955-0.2083-0.061-00.31810.00180.00590.2929-0.04950.3592-1.061422.6409-28.6634
120.0376-0.09790.0580.0318-0.04480.27610.08720.09750.10050.238-0.0940.1422-0.0210.0568-00.3673-0.02660.00210.3584-0.05530.288413.176811.708-21.3546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:331)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 332:486)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 487:513)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 514:542)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 4:45)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 46:118)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 119:275)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 276:341)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 342:406)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 407:486)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 487:513)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 514:543)

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